High-throughput RNA sequencing analysis of Mallotus japonicus revealed novel polerovirus and amalgavirus.

High-throughput RNA sequencing (RNA-seq) analysis of samples from Mallotus japonicus, a traditional medicinal plant, yielded two novel RNA viruses tentatively named Mallotus japonicus virus A (MjVA) and Mallotus japonicus virus B (MjVB). The MjVA and MjVB genomes encode proteins showing amino acid sequence similarities to those of poleroviruses (the genus Polerovirus, the family Solemoviridae) and amalgaviruses (the genus Amalgavirus, the family Amalgaviridae), respectively. The MjVA genome contains seven highly overlapping open reading frames, which are translated to seven proteins through various translational mechanisms, including -1 programmed ribosomal frameshifting (PRF) at the slippery motif GGGAAAC, non-AUG translational initiation, and stop codon readthrough. The MjVB genome encodes two proteins; one of which is translated by +1 PRF mechanism at the slippery motif UUUCGN. The abundance analysis of virus-derived RNA fragments revealed that MjVA is highly concentrated in plant parts with well-developed phloem tissues as previously demonstrated in other poleroviruses, which are transmitted by phloem feeders, such as aphids. MjVB, an amalgavirus generally transmitted by seeds, is distributed in all samples at low concentrations. Thus, this study demonstrates the effectiveness and usefulness of RNA-seq analysis of plant samples for the identification of novel RNA viruses and analysis of their tissue distribution. Keywords: Polerovirus; Amalgavirus; Mallotus japonicus; RNA virus; viral genome; programmed ribosomal frameshifting.

A novel RNA virus, Thesium chinense closterovirus 1, identified by high-throughput RNA-sequencing of the parasitic plant Thesium chinense.

The genome sequence of a closterovirus (genus Closterovirus, family Closteroviridae), tentatively named Thesium chinense closterovirus 1 (TcCV1), was identified by performing high-throughput RNA-sequencing of the haustoria and root tissues of Thesium chinense, a parasitic plant. The TcCV1 genome was predicted to encode nine proteins, eight of which have orthologs in previously identified closteroviruses. The TcCV1 RNA-dependent RNA polymerase (RdRp) and heat shock protein 70 homolog (Hsp70h) showed 27.8-68.2% and 23.8-55.1% amino acid identity, respectively, to orthologous proteins of known closteroviruses. The putative +1 ribosomal frameshifting site required for producing RdRp was identified as GUUUAGC with UAG stop codon and the skipped nucleotide U. Phylogenetic trees based on RdRp and Hsp70h show that TcCV1 is a novel member of the genus Closterovirus, forming a subclade with a group of known closteroviruses, including mint virus 1 and carnation necrotic fleck virus. The genome sequence of TcCV1 may be useful for studying the genome evolution of closteroviruses. Keywords: Thesium chinense closterovirus 1; Closterovirus; Closteroviridae; Thesium chinense.

Artemisia capillaris nucleorhabdovirus 1, a novel member of the genus Alphanucleorhabdovirus, identified in the Artemisia capillaris transcriptome.

A novel, negative-sense, single-stranded RNA virus, Artemisia capillaris nucleorhabdovirus 1 (AcNRV1), was identified in the transcriptome data of Artemisia capillaris (commonly known as capillary wormwood) root tissue. The AcNRV1 genome contains six open reading frames encoding a nucleocapsid (N), phosphoprotein, movement protein P3, matrix protein, glycoprotein, and polymerase (L). Sequence comparison and phylogenetic analysis using L and N protein sequences revealed that AcNRV1 is a novel member of the genus Alphanucleorhabdovirus, one of the six plant-infecting rhabdovirus genera of the family Rhabdoviridae. Wheat yellow striate virus and rice yellow stunt virus were identified as the closest known rhabdoviruses of AcNRV1. The conserved regulatory sequences involved in transcription termination/polyadenylation (TTP) and transcription initiation (TI) of individual genes were identified in the AcNRV1 genome with the consensus sequence 3'-(A/U)UUAUUUUU-GGG-UUG-5' (in the negative-sense genome), whereby dashes separate the TTP, untranscribed intergenic spacer, and TI elements. The AcNRV1 genome sequence will contribute to further understanding the genome structural evolution of plant rhabdoviruses. Keywords: Artemisia capillaris nucleorhabdovirus 1; plant virus; Alphanucleorhabdovirus; Rhabdoviridae.

Identification of dicistro-like viruses in the transcriptome data of Striga asiatica and other plants.

Dicistroviruses (the family Dicistroviridae) are positive-sense single-stranded RNA viruses of the order Picornavirales, which is a rapidly growing viral group. They have been detected in a wide range of animals, predominantly in insects and crustaceans. In this study, we identified the genome sequences of 14 dicistro-like viruses in the transcriptome data from 12 plant species, including Striga asiatica dicistro-like virus 1 and 2 identified in the transcriptome data of Striga asiatica. Sequence comparison and phylogenetic analysis indicated that these 14 plant-associated dicistro-like viruses were novel members of the family Dicistroviridae, five of which are placed within the genera Aparavirus and Cripavirus, which mainly consist of viruses infecting animals, including insects. The other nine plant dicistro-like viruses formed clades with unclassified dicistroviruses. Our study implies that a wide range of plant species may serve as hosts for dicistroviruses or reservoirs for their transmission. Keywords: dicistrovirus; Dicistroviridae; plant; transcriptome; Striga asiatica.

Two novel poty-like viruses identified from the transcriptome data of purple witchweed (Striga hermonthica).

Potyvirids (the family Potyviridae) are the largest family of plant RNA viruses. Two novel potyvirid viruses, Striga-associated poty-like virus 1 (SaPlV1) and Striga-associated poty-like virus 2 (SaPlV2), were identified from the transcriptome data of purple witchweed (Striga hermonthica). SaPlV1 was most closely related to bellflower veinal mottle virus (BVMoV), the only member of the genus Bevemovirus, and then to macluraviruses (the genus Macluravirus). The SaPlV1 genome encodes a 2462-amino acid (aa) polyprotein that may be cleaved into nine mature peptides. The cleavage sites of SaPlV1, BVMoV, and macluravirus polyproteins shared strong sequence similarities. SaPlV2 was most closely related to celery latent virus, the sole species of the genus Celavirus, which is the most divergent potyvirid genus. The SaPlV2 polyprotein contained 3329 aa and it may be cleaved into at least seven or eight mature peptides. Phylogenetic analysis suggested that SaPlV1 and SaPlV2 may be novel species of the genera Bevemovirus and Celavirus, respectively. The genome sequences of SaPlV1 and SaPlV2 are useful resources for studying the genome evolution of potyvirids. Keywords: Striga-associated poty-like virus 1; Striga-associated poty-like virus 2; Potyviridae; Beve- movirus; Celavirus; purple witchweed; Striga hermonthica.

Identification of the genome sequence of Zostera associated varicosavirus 1, a novel negative-sense RNA virus, in the common eelgrass (Zostera marina) transcriptome.

Varicosaviruses (the genus Varicosavirus) are bipartite, negative-sense, single-stranded RNA viruses that infect plants. We analyzed a transcriptome dataset isolated from the common eelgrass (Zostera marina) and identified a novel varicosavirus named Zostera associated varicosavirus 1 (ZaVV1). The ZaVV1 genome consists of two genomic segments: RNA1 (6,632-nt) has an open reading frame (ORF) encoding a large multi-functional polymerase protein (L), while RNA2 (4,304-nt) has four ORFs: one for a nucleocapsid protein and three for proteins with unknown functions (P2, P3, and P4). Sequence comparison and phylogenetic analysis using L proteins showed that ZaVV1 is a novel member of the genus Varicosavirus of the family Rhabdoviridae. The conserved regulatory elements involved in transcription termination/polyadenylation and transcription initiation were identified in the ZaVV1 gene-junction regions with the consensus sequence 3'-UAUUAUUCUUUUUGCUCU-5' (in the negative-sense genome). The ZaVV1 genome sequence may be useful for studying the phylogenetic relationships of varicosaviruses and genome evolution of rhabdoviruses. Keywords: Zostera associated varicosavirus 1; Varicosavirus; Rhabdoviridae; common eelgrass; Zostera marina.